Hepatitis C virus (HCV) infects ~185 million people worldwide; more than 4 million Americans. HCV infection is the most common cause of liver disease (cirrhosis), is the leading indicator for liver transplantation (LT), and is a potent driver of hepatocellular carcinoma (HCC). There are no effective therapies for HCC and 5- year survival is <12%, emphasizing the dire need for novel preventative strategies. New direct-acting antivirals have generated enormous optimism about controlling HCV infection, but risk for HCC remains elevated even after cure. While there have been significant improvements over the last 30 years, long-term survival of LT recipients is limited by the near universal recurrence of HCV and accelerated progression to cirrhosis due to a lack of non-invasive markers of disease progression. There is no definitive evidence that HCV directly mediates genetic damage, however there is growing evidence for early and progressive epigenetic changes, particularly in DNA methylation (5mC) and hydroxymethylation (5hmC), during liver disease. Global losses and gene-specific increases in DNA epigenetic marks are common during inflammation, cirrhosis, and HCC. Cirrhosis is a well-defined precancerous condition, yet its molecular underpinnings at the level of the epigenome have not been examined. Preliminary and published DNA epigenetic mark profiling in cirrhotic liver and HCC by our group revealed that hundreds of genes displayed abnormal 5mC and 5hmC patterns between normal and diseased states, with 5hmC particularly affected during cirrhosis. Based on these preliminary data, we propose three specific aims to test the hypothesis that altered DNA epigenetic marks caused by HCV infection drive liver disease and hepatocarcinogenesis. Identification of these defects and their mechanistic underpinnings is expected to yield new therapeutic targets and clinical markers. We further propose that the elevated HCC risk after cure is due, in part, to epigenetic `scars' left by HCV infection, which also represent a clinically targetable entity. In aim 1 we will define how HCV infection impacts DNA marks and transcription globally in primary liver cirrhosis and relate these to patient clinical data to define HCV infection-specific defects. In aim 2, we will investigate the earliest stages of HCV infection in serial liver biopsies from LT patients to define the evolution of DNA epigenetic mark changes and, by integrating findings with aims 1 and 3, define HCV-specific epigenetic signatures that serve as useful markers of liver injury. Finally, in aim 3 we will use a novel immortalized hepatocyte cell culture model to define mechanistically how HCV modulates the epigenome to drive transformation. Results from these studies are expected to greatly enhance our understanding of how a widespread infectious agent, coupled with ubiquitous chronic inflammation, influence DNA epigenetic marks in a way that drives transformation. Our studies should also yield completely new information on both the acute and chronic phases of HCV infection, providing new targets for therapy, diagnosis, and prognosis.